High-Resolution Profiling of Histone Methylations in the Human Genome
Combinatorial patterns of histone acetylations and methylations in the human genome
The data suggest that a large number of histone modifications may act cooperatively to prepare chromatin for transcriptional activation and be associated with promoters and enhancers.
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
- C. Zang, Dustin E. Schones, Chen Zeng, Kairong Cui, K. Zhao, Weiqun Peng
- 1 August 2009
Based on the biological observation that histone modifications tend to cluster to form domains, a method that identifies spatial clusters of signals unlikely to appear by chance is presented that outperforms existing methods in the identification of ChIP-enriched signals for histone modification profiles.
Dynamic Regulation of Nucleosome Positioning in the Human Genome
Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes
Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells.
Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells
This study shows in mouse ES cells that Tet1 is preferentially bound to CpG-rich sequences at promoters of both transcriptionally active and Polycomb-repressed genes, and reveals a dual function of Tet1 in promoting transcription of pluripotency factors as well as participating in the repression ofPolycomb-targeted developmental regulators.
Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes
Genome-wide identification of in vivo protein–DNA binding sites from ChIP-Seq data
- Raja Jothi, Suresh Cuddapah, A. Barski, Kairong Cui, K. Zhao
- BiologyNucleic Acids Research
- 6 August 2008
Using tag density as an indicator of DNA-binding affinity, it is shown that tag densities at the binding sites are a good indicator of protein–DNA binding affinity, which could be used to distinguish and characterize strong and weak binding sites.
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.
- Suresh Cuddapah, Raja Jothi, Dustin E. Schones, Tae-Young Roh, Kairong Cui, K. Zhao
- BiologyGenome Research
- 1 December 2008
The data indicate that C TCF may play important roles in the barrier activity of insulators, and this study provides a resource for further investigation of the CTCF function in organizing chromatin in the human genome.